#Conet cytoscape install#

#Conet cytoscape install#

You can install CoNet from the Cytoscape App Store or from CoNet's website where you can also find Tutorials and Documentation. CoNet runs on command line and as a Cytoscape plugin It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). We focus on the development of computational methods for the analysis of (next-generation) sequence data and the investigation of community properties from metagenomics, metatranscriptomics and meta-metabolomics data.ĬoNet is a tool that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. Using in vitro synthetic ecology apporaches, we investigate modulation strategies to be developed in novel microbiota-based therapies, ranging from diet, pre- and (next-gen)probiotics, faecal transplants as well as drugs. In addition, we integrate metagenomics, metatranscriptomics and meta-metabolomics data to study functional consequences of dysbiosis. In this context, we recently discovered the existence of gut flora types (enterotypes) linked to diet, motility and inflammation and are studying the predictive power of microbial markers for various intestinal diseases (auto-immune, neurological and metabolic pathologies as well as cancer). Studying the complexity of the human ecosystem at this resolution allowed the birth of a new, exciting subfield in computational biology which will eventually allow classical, cellular-level systems biology to progress towards modeling entire communities (“ecosystems biology”) and untangling interspecies networks of competition, collaboration and communication at the molecular level.Īt the same time, human cohort and intervention studies allow important insights in the functioning and variability of the healthy human microbiome and its components and investigate its alteration in disease. These advances have allowed the initiation of the International Human Microbiome Project, aiming at genomically characterizing the totality of human-associated micro-organisms (the “microbiome”).

Recent technological advances such as metagenomics and next-generation sequencing make it possible, for the first time, to study the various microbiota of the human body at a previously unseen scale. The Raes Lab combines large-scale sequencing, cohort studies, microbiology and synthetic ecology with computational approaches to investigate the functioning and variability of the human microbiome and study its alteration and modulation in disease.